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First, thank you for your help.

I've been using *nix for 5 years now, and this has always bothered me:

I cannot select text in two terminals, without clearing the first selection as soon as I select in the second terminal.

This is true with gnome-terminal, xfce-terminal, and terminator. So I'm starting to think this is a restriction in GTK or X or something.

Is it possible for me to keep as many selections highlighted as I want to?

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X has two buffers, a primary and a secondary; with which of these which application communicates depends on a variety of things.

So no, you can't have selections active in multiple xterms.

You could use something like parcelite and script it to write stuff out to a file so all your selections end up in one spot.

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Hm, so I forgot to mention, but if I have multiple gvim windows open, I can select in multiple gvim windows. Like you said I can have only 1 active selection. However, earlier selections will be underlined (depends on vimrc settings). This underline still helps me visually. Not sure why terminals have to completely clear previous selections. – David Apr 30 '13 at 0:20

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